def copy_study(
self,
src_uuid: str,
dest_study_name: str,
group_ids: List[str],
params: RequestParameters,
) -> str:
src_study = self._get_study(src_uuid)
self._assert_permission(params.user, src_study,
StudyPermissionType.READ)
if not isinstance(src_study, RawStudy):
raise StudyTypeUnsupported(
f"Study {src_uuid} with type {src_study.type} not recognized")
dest_study = deepcopy(src_study)
dest_study.id = str(uuid4())
dest_study.name = dest_study_name
dest_study.workspace = DEFAULT_WORKSPACE_NAME
dest_study.path = str(self.study_service.get_default_workspace_path() /
dest_study.id)
study = self.study_service.copy_study(src_study, dest_study)
self._save_study(study, params.user, group_ids)
self.event_bus.push(
Event(EventType.STUDY_CREATED, study.to_json_summary()))
return str(study.id)
def get_study_information(self, uuid: str,
params: RequestParameters) -> JSON:
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.READ)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
return self.study_service.get_study_information(study)
def get_matrix(self, route: str, params: RequestParameters) -> bytes:
uuid, path = StorageServiceUtils.extract_info_from_url(route)
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.READ)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
return self.exporter_service.get_matrix(study, path)
def get(self, route: str, depth: int, params: RequestParameters) -> JSON:
uuid, url = StorageServiceUtils.extract_info_from_url(route)
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.READ)
if isinstance(study, RawStudy):
return self.study_service.get(study, url, depth)
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
def import_output(self, uuid: str, stream: IO[bytes],
params: RequestParameters) -> JSON:
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.RUN)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
res = self.importer_service.import_output(study, stream)
return res
def delete_output(self, uuid: str, output_name: str,
params: RequestParameters) -> None:
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.WRITE)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
self.study_service.delete_output(study, output_name)
self.event_bus.push(
Event(EventType.STUDY_EDITED, study.to_json_summary()))
def edit_study(self, route: str, new: JSON,
params: RequestParameters) -> JSON:
uuid, url = StorageServiceUtils.extract_info_from_url(route)
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.WRITE)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
updated = self.study_service.edit_study(study, url, new)
self.event_bus.push(
Event(EventType.STUDY_EDITED, study.to_json_summary()))
return updated
def upload_matrix(self, path: str, data: bytes,
params: RequestParameters) -> None:
uuid, matrix_path = StorageServiceUtils.extract_info_from_url(path)
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.WRITE)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
self.importer_service.upload_matrix(study, matrix_path, data)
self.event_bus.push(
Event(EventType.STUDY_EDITED, study.to_json_summary()))
def export_study(
self,
uuid: str,
params: RequestParameters,
outputs: bool = True,
) -> BytesIO:
study = self._get_study(uuid)
self._assert_permission(params.user, study, StudyPermissionType.READ)
if not isinstance(study, RawStudy):
raise StudyTypeUnsupported(
f"Study {uuid} with type {study.type} not recognized")
return self.exporter_service.export_study(study, outputs)